powerpkg (version 1.6)

plotNtdt: A function for plotting the results from ntdt.q

Description

This function plots the results from ntdt.q

Usage

plotNtdt(g, m, alpha = 5e-08, power = 0.8,...)

Arguments

g

the genotype risk ratio for the susceptibility gene

m

the frequency of the marker allele in linkage disequilibrium with the susceptibility allele.

alpha

the Type 1 error rate

power

the desired power

...

additional arguments for plot

Value

A plot of the results generated by a call to the ntdt.q() function.

Details

We will use an R program that implements the power formulae of Abel and Muller-Myhsok (1998). These formulae allow one to quickly compute power of the TDT approach under a variety of different conditions. This R program was modeled on Martin Farrall's Mathematica notebook.

The power computations here use a simple genetic model with several aspects: (1) The disease locus has two alleles, A and a, with allele frequencies q and 1-q. The risk of disease follows a multiplicative model with genotype relative risks of g and g*g for the A/a and A/A subjects. (2) There is a perfectly linked marker with two alleles, with allele frequencies m and 1-m.

References

Abel L, Muller-Myhsok B. Maximum-likelihood expression of the transmission/disequilibrium test and power considerations. Am J Hum Genet. 1998 Aug;63(2):664-7.

Chen WM, Deng HW. A general and accurate approach for computing the statistical power of the transmission disequilibrium test for complex disease genes. Genet Epidemiol. 2001 Jul;21(1):53-67.

Iles MM. On calculating the power of a TDT study--comparison of methods. Ann Hum Genet. 2002 Jul;66(Pt 4):323-8.

Purcell S, Cherny SS, Sham PC. Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits. Bioinformatics. 2003 Jan;19(1):149-50.

See Also

ntdt, ntdt.q

Examples

# NOT RUN {
## Duplicate Figures 1 and 2 from Abel and Muller-Myhsok (1998)
## Am J Hum Genet 63:664-667
plotNtdt(g=2,m=0.10) 
## gives Figure 1A
plotNtdt(g=2,m=0.50) 
## gives Figure 1B
# }